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R/match_motifs.R
In motifmatchr: Fast Motif Matching in R
Defines functions
matchMotifs_helper
#' motifMatches
#'
#' get motif matches from SummarizedExperiment object
#' @param object SummarizedExperiment object with matches assay
#' @return matrix with scores
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19")
#'
#' motifMatches(motif_ix)
setGeneric("motifMatches", function(object) standardGeneric("motifMatches"))
#' @describeIn motifMatches method for SummarizedExperiment
#' @export
setMethod("motifMatches", c(object = "SummarizedExperiment"),
function(object) {
if ("motifMatches" %ni% assayNames(object)){
if ("motif_matches" %in% assayNames(object)){
warning("motif_matches assay name deprecated",
"motifmatchr now using motifMatches")
return(assays(object)$motif_matches)
}
stop("No motifMatches in this object")
}
assays(object)$motifMatches
})
#' motifScores
#'
#' get motif scores from SummarizedExperiment object
#' @param object SummarizedExperiment object with scores assay
#' @return matrix with scores
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19",
#' out = "scores")
#'
#' motifScores(motif_ix)
setGeneric("motifScores", function(object) standardGeneric("motifScores"))
#' @describeIn motifScores method for SummarizedExperiment
#' @export
setMethod("motifScores", c(object = "SummarizedExperiment"), function(object) {
if ("motifScores" %ni% assayNames(object)){
if ("motif_scores" %in% assayNames(object)){
warning("motif_scores assay name deprecated",
"motifmatchr now using motifScores")
return(assays(object)$motif_scores)
}
stop("No motifScores in this object")
}
assays(object)$motifScores
})
#' motifCounts
#'
#' get motif counts from SummarizedExperiment object
#' @param object SummarizedExperiment object with counts assay
#' @return matrix with counts
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19",
#' out = "scores")
#'
#' motifCounts(motif_ix)
setGeneric("motifCounts", function(object) standardGeneric("motifCounts"))
#' @describeIn motifCounts method for SummarizedExperiment
#' @export
setMethod("motifCounts", c(object = "SummarizedExperiment"), function(object) {
if ("motifCounts" %ni% assayNames(object)){
if ("motif_counts" %in% assayNames(object)){
warning("motif_counts assay name deprecated",
"motifmatchr now using motifCounts")
return(assays(object)$motif_counts)
}
stop("No motifCounts in this object")
}
assays(object)$motifCounts
})
matchMotifs_helper <- function(pwms, seqs, bg, p.cutoff, w, out, ranges) {
motif_mats <- convert_pwms(pwms, bg)
if (out == "matches") {
tmp_out <- get_motif_ix(motif_mats, seqs, bg, p.cutoff, w)
if (is.null(ranges)) {
out <- SummarizedExperiment(assays =
list(motifMatches = as(tmp_out,
"lMatrix")),
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
} else {
out <- SummarizedExperiment(assays =
list(motifMatches = as(tmp_out,
"lMatrix")),
rowRanges = ranges,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
}
} else if (out == "scores") {
tmp_out <- get_motif_ix_plus(motif_mats, seqs, bg, p.cutoff, w)
tmp_out$motifMatches <- as(tmp_out$motifMatches, "lMatrix")
if (is.null(ranges)) {
out <- SummarizedExperiment(assays = tmp_out,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
} else {
out <- SummarizedExperiment(assays = tmp_out,
rowRanges = ranges,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
}
} else {
tmp_out <- get_motif_positions(motif_mats, seqs, bg, p.cutoff, w)
if (is.null(ranges)) {
out <- lapply(1:length(motif_mats), function(x) {
m_ix <- which(tmp_out$motif_ix == x - 1)
IRangesList(lapply(seq_along(seqs),
function(y){
ms_ix <- m_ix[which(tmp_out$seq_ix[m_ix] == y -1)]
tmp <- IRanges(start = tmp_out$pos[ms_ix] + 1,
width = ncol(motif_mats[[x]]))
mcols(tmp) <- DataFrame(strand = tmp_out$strand[ms_ix],
score = tmp_out$score[ms_ix])
tmp
}))
})
names(out) <- names(pwms)
} else {
out <- lapply(1:length(motif_mats), function(x) {
m_ix <- which(tmp_out$motif_ix == x - 1)
GRanges(seqnames(ranges)[tmp_out$seq_ix[m_ix] + 1],
IRanges(start =
start(ranges[tmp_out$seq_ix[m_ix] + 1]) +
tmp_out$pos[m_ix],
width = ncol(motif_mats[[x]])),
strand = tmp_out$strand[m_ix],
score = tmp_out$score[m_ix])
})
names(out) <- names(pwms)
out <- GRangesList(out)
}
}
return(out)
}
#' matchMotifs
#'
#' Find motif matches
#' @param pwms either \code{\link[TFBSTools]{PFMatrix}},
#' \code{\link[TFBSTools]{PFMatrixList}}, \code{\link[TFBSTools]{PWMatrix}},
#' \code{\link[TFBSTools]{PWMatrixList}}
#' @param subject either \code{\link[GenomicRanges]{GenomicRanges}},
#' \code{\link[Biostrings]{DNAStringSet}}, \code{\link[Biostrings]{DNAString}},
#' or character vector
#' @param genome BSgenome object, \code{\link[Biostrings]{DNAStringSet}}, or
#' \code{\link[Rsamtools]{FaFile}}, or short string signifying genome build
#' recognized by \code{\link[BSgenome]{getBSgenome}}. Only required if
#' subject is \code{\link[GenomicRanges]{GenomicRanges}} or
#' \code{\link[SummarizedExperiment]{RangedSummarizedExperiment}} or if bg is set
#' to "genome"
#' @param bg background nucleotide frequencies. Default is to compute based on
#' subject, i.e. the specific set of sequences being evaluated. See Details.
#' @param out what to return? see return section
#' @param p.cutoff p-value cutoff for returning motifs
#' @param w parameter controlling size of window for filtration; default is 7
#' @param ranges if subject is not GenomicRanges or RangedSummarizedExperiment,
#' these ranges can be used to specify what ranges the input sequences
#' correspond to. These ranges will be incorporated into the
#' SummarizedExperiment output if out is "matches" or "scores" or will be used
#' to give absolute positions of motifs if out is "positions"
#' @param ... additional arguments depending on inputs
#' @details Background nucleotide frequencies can be set to "subject" to use the
#' subject sequences or ranges for computing the nucleotide frequencies,
#' "genome" for using the genomice frequencies (in which case a genome must be
#' specified), "even" for using 0.25 for each base, or a numeric vector with A,
#' C, G, and T frequencies.
#' @return Either returns a SummarizedExperiment with a sparse matrix with
#' values set to TRUE for a match (if out == 'matches'), a
#' SummarizedExperiment with a matches matrix as well as matrices with the
#' maximum motif score and total motif counts (if out == 'scores'), or a
#' \code{\link[GenomicRanges]{GenomicRangesList}} or a list of
#' \code{\link[IRanges]{IRangesList}} with all the positions of matches
#' (if out == 'positions')
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks, genome = "BSgenome.Hsapiens.UCSC.hg19")
#'
setGeneric("matchMotifs",
function(pwms, subject, ...) standardGeneric("matchMotifs"))
#' @describeIn matchMotifs PWMatrixList/DNAStringSet
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "DNAStringSet"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/character
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "character"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
matchMotifs_helper(pwms, subject, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/DNAString
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "DNAString"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/GenomicRanges
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "GenomicRanges"),
function(pwms,
subject,
genome = GenomeInfoDb::genome(subject),
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
GenomicRanges::strand(subject) <- "+"
genome <- validate_genome_input(genome)
seqs <- getSeq(genome, subject)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, seqs, genome)
}
seqs <- as.character(seqs)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, subject)
})
#' @describeIn matchMotifs PWMatrixList/RangedSummarizedExperiment
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "RangedSummarizedExperiment"),
function(pwms, subject,
genome = GenomeInfoDb::genome(subject),
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
matchMotifs(pwms, rowRanges(subject),
genome = genome,
bg = bg,
out = out,
p.cutoff = p.cutoff,
w = w)
})
#' @describeIn matchMotifs PWMatrixList/BSGenomeViews
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "BSgenomeViews"),
function(pwms,
subject,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
seqs <- as.character(subject)
ranges <- BSgenome::granges(subject)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, BSgenome::subject(subject))
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
### PFMatrixList ---------------------------------------------------------------
#' @describeIn matchMotifs PFMatrixList/ANY
#' @export
setMethod("matchMotifs", signature(pwms = "PFMatrixList", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- do.call(PWMatrixList, lapply(pwms, toPWM))
matchMotifs(pwms_list,
subject,
...)
})
# Single PWM input -------------------------------------------------------------
#' @describeIn matchMotifs PWMatrix/ANY
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrix", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- PWMatrixList(pwms)
matchMotifs(pwms_list,
subject,
...)
})
# Single PFM -------------------------------------------------------------------
#' @describeIn matchMotifs PFMatrix/ANY
#' @export
setMethod("matchMotifs",
signature(pwms = "PFMatrix", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- PWMatrixList(toPWM(pwms))
matchMotifs(pwms_list,
subject,
...)
})
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Defines functions matchMotifs_helper
#' motifMatches
#'
#' get motif matches from SummarizedExperiment object
#' @param object SummarizedExperiment object with matches assay
#' @return matrix with scores
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19")
#'
#' motifMatches(motif_ix)
setGeneric("motifMatches", function(object) standardGeneric("motifMatches"))
#' @describeIn motifMatches method for SummarizedExperiment
#' @export
setMethod("motifMatches", c(object = "SummarizedExperiment"),
function(object) {
if ("motifMatches" %ni% assayNames(object)){
if ("motif_matches" %in% assayNames(object)){
warning("motif_matches assay name deprecated",
"motifmatchr now using motifMatches")
return(assays(object)$motif_matches)
}
stop("No motifMatches in this object")
}
assays(object)$motifMatches
})
#' motifScores
#'
#' get motif scores from SummarizedExperiment object
#' @param object SummarizedExperiment object with scores assay
#' @return matrix with scores
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19",
#' out = "scores")
#'
#' motifScores(motif_ix)
setGeneric("motifScores", function(object) standardGeneric("motifScores"))
#' @describeIn motifScores method for SummarizedExperiment
#' @export
setMethod("motifScores", c(object = "SummarizedExperiment"), function(object) {
if ("motifScores" %ni% assayNames(object)){
if ("motif_scores" %in% assayNames(object)){
warning("motif_scores assay name deprecated",
"motifmatchr now using motifScores")
return(assays(object)$motif_scores)
}
stop("No motifScores in this object")
}
assays(object)$motifScores
})
#' motifCounts
#'
#' get motif counts from SummarizedExperiment object
#' @param object SummarizedExperiment object with counts assay
#' @return matrix with counts
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks,
#' genome = "BSgenome.Hsapiens.UCSC.hg19",
#' out = "scores")
#'
#' motifCounts(motif_ix)
setGeneric("motifCounts", function(object) standardGeneric("motifCounts"))
#' @describeIn motifCounts method for SummarizedExperiment
#' @export
setMethod("motifCounts", c(object = "SummarizedExperiment"), function(object) {
if ("motifCounts" %ni% assayNames(object)){
if ("motif_counts" %in% assayNames(object)){
warning("motif_counts assay name deprecated",
"motifmatchr now using motifCounts")
return(assays(object)$motif_counts)
}
stop("No motifCounts in this object")
}
assays(object)$motifCounts
})
matchMotifs_helper <- function(pwms, seqs, bg, p.cutoff, w, out, ranges) {
motif_mats <- convert_pwms(pwms, bg)
if (out == "matches") {
tmp_out <- get_motif_ix(motif_mats, seqs, bg, p.cutoff, w)
if (is.null(ranges)) {
out <- SummarizedExperiment(assays =
list(motifMatches = as(tmp_out,
"lMatrix")),
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
} else {
out <- SummarizedExperiment(assays =
list(motifMatches = as(tmp_out,
"lMatrix")),
rowRanges = ranges,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
}
} else if (out == "scores") {
tmp_out <- get_motif_ix_plus(motif_mats, seqs, bg, p.cutoff, w)
tmp_out$motifMatches <- as(tmp_out$motifMatches, "lMatrix")
if (is.null(ranges)) {
out <- SummarizedExperiment(assays = tmp_out,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
} else {
out <- SummarizedExperiment(assays = tmp_out,
rowRanges = ranges,
colData =
DataFrame(name = name(pwms),
row.names = names(pwms)))
}
} else {
tmp_out <- get_motif_positions(motif_mats, seqs, bg, p.cutoff, w)
if (is.null(ranges)) {
out <- lapply(1:length(motif_mats), function(x) {
m_ix <- which(tmp_out$motif_ix == x - 1)
IRangesList(lapply(seq_along(seqs),
function(y){
ms_ix <- m_ix[which(tmp_out$seq_ix[m_ix] == y -1)]
tmp <- IRanges(start = tmp_out$pos[ms_ix] + 1,
width = ncol(motif_mats[[x]]))
mcols(tmp) <- DataFrame(strand = tmp_out$strand[ms_ix],
score = tmp_out$score[ms_ix])
tmp
}))
})
names(out) <- names(pwms)
} else {
out <- lapply(1:length(motif_mats), function(x) {
m_ix <- which(tmp_out$motif_ix == x - 1)
GRanges(seqnames(ranges)[tmp_out$seq_ix[m_ix] + 1],
IRanges(start =
start(ranges[tmp_out$seq_ix[m_ix] + 1]) +
tmp_out$pos[m_ix],
width = ncol(motif_mats[[x]])),
strand = tmp_out$strand[m_ix],
score = tmp_out$score[m_ix])
})
names(out) <- names(pwms)
out <- GRangesList(out)
}
}
return(out)
}
#' matchMotifs
#'
#' Find motif matches
#' @param pwms either \code{\link[TFBSTools]{PFMatrix}},
#' \code{\link[TFBSTools]{PFMatrixList}}, \code{\link[TFBSTools]{PWMatrix}},
#' \code{\link[TFBSTools]{PWMatrixList}}
#' @param subject either \code{\link[GenomicRanges]{GenomicRanges}},
#' \code{\link[Biostrings]{DNAStringSet}}, \code{\link[Biostrings]{DNAString}},
#' or character vector
#' @param genome BSgenome object, \code{\link[Biostrings]{DNAStringSet}}, or
#' \code{\link[Rsamtools]{FaFile}}, or short string signifying genome build
#' recognized by \code{\link[BSgenome]{getBSgenome}}. Only required if
#' subject is \code{\link[GenomicRanges]{GenomicRanges}} or
#' \code{\link[SummarizedExperiment]{RangedSummarizedExperiment}} or if bg is set
#' to "genome"
#' @param bg background nucleotide frequencies. Default is to compute based on
#' subject, i.e. the specific set of sequences being evaluated. See Details.
#' @param out what to return? see return section
#' @param p.cutoff p-value cutoff for returning motifs
#' @param w parameter controlling size of window for filtration; default is 7
#' @param ranges if subject is not GenomicRanges or RangedSummarizedExperiment,
#' these ranges can be used to specify what ranges the input sequences
#' correspond to. These ranges will be incorporated into the
#' SummarizedExperiment output if out is "matches" or "scores" or will be used
#' to give absolute positions of motifs if out is "positions"
#' @param ... additional arguments depending on inputs
#' @details Background nucleotide frequencies can be set to "subject" to use the
#' subject sequences or ranges for computing the nucleotide frequencies,
#' "genome" for using the genomice frequencies (in which case a genome must be
#' specified), "even" for using 0.25 for each base, or a numeric vector with A,
#' C, G, and T frequencies.
#' @return Either returns a SummarizedExperiment with a sparse matrix with
#' values set to TRUE for a match (if out == 'matches'), a
#' SummarizedExperiment with a matches matrix as well as matrices with the
#' maximum motif score and total motif counts (if out == 'scores'), or a
#' \code{\link[GenomicRanges]{GenomicRangesList}} or a list of
#' \code{\link[IRanges]{IRangesList}} with all the positions of matches
#' (if out == 'positions')
#' @export
#' @examples
#'
#' data(example_motifs, package = "motifmatchr")
#'
#' # Make a set of peaks
#' peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
#' ranges = IRanges::IRanges(start = c(76585873,42772928,
#' 100183786),
#' width = 500))
#'
#' # Get motif matches for example motifs
#' motif_ix <- matchMotifs(example_motifs, peaks, genome = "BSgenome.Hsapiens.UCSC.hg19")
#'
setGeneric("matchMotifs",
function(pwms, subject, ...) standardGeneric("matchMotifs"))
#' @describeIn matchMotifs PWMatrixList/DNAStringSet
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "DNAStringSet"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/character
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "character"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
matchMotifs_helper(pwms, subject, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/DNAString
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "DNAString"),
function(pwms,
subject,
genome = NULL,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7, ranges = NULL) {
out <- match.arg(out)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, genome)
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
#' @describeIn matchMotifs PWMatrixList/GenomicRanges
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "GenomicRanges"),
function(pwms,
subject,
genome = GenomeInfoDb::genome(subject),
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
GenomicRanges::strand(subject) <- "+"
genome <- validate_genome_input(genome)
seqs <- getSeq(genome, subject)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, seqs, genome)
}
seqs <- as.character(seqs)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, subject)
})
#' @describeIn matchMotifs PWMatrixList/RangedSummarizedExperiment
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "RangedSummarizedExperiment"),
function(pwms, subject,
genome = GenomeInfoDb::genome(subject),
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
matchMotifs(pwms, rowRanges(subject),
genome = genome,
bg = bg,
out = out,
p.cutoff = p.cutoff,
w = w)
})
#' @describeIn matchMotifs PWMatrixList/BSGenomeViews
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrixList",
subject = "BSgenomeViews"),
function(pwms,
subject,
bg = c("subject","genome","even"),
out = c("matches", "scores", "positions"),
p.cutoff = 5e-05, w = 7) {
out <- match.arg(out)
seqs <- as.character(subject)
ranges <- BSgenome::granges(subject)
if (is.numeric(bg)){
bg <- check_bg(bg)
} else{
bg_method <- match.arg(bg)
bg <- get_bg(bg_method, subject, BSgenome::subject(subject))
}
seqs <- as.character(subject)
matchMotifs_helper(pwms, seqs, bg, p.cutoff, w, out, ranges)
})
### PFMatrixList ---------------------------------------------------------------
#' @describeIn matchMotifs PFMatrixList/ANY
#' @export
setMethod("matchMotifs", signature(pwms = "PFMatrixList", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- do.call(PWMatrixList, lapply(pwms, toPWM))
matchMotifs(pwms_list,
subject,
...)
})
# Single PWM input -------------------------------------------------------------
#' @describeIn matchMotifs PWMatrix/ANY
#' @export
setMethod("matchMotifs", signature(pwms = "PWMatrix", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- PWMatrixList(pwms)
matchMotifs(pwms_list,
subject,
...)
})
# Single PFM -------------------------------------------------------------------
#' @describeIn matchMotifs PFMatrix/ANY
#' @export
setMethod("matchMotifs",
signature(pwms = "PFMatrix", subject = "ANY"),
function(pwms,
subject,
...) {
pwms_list <- PWMatrixList(toPWM(pwms))
matchMotifs(pwms_list,
subject,
...)
})
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